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name python-package-dev description Python research package development with pyproject.toml, testing with pytest, documentation with Sphinx, and publishing to PyPI for academic software. tags ["python-packaging","pyproject-toml","pytest","sphinx","scientific-software"] version 1.0.0 authors ["@xjtulyc"] license MIT platforms ["claude-code","codex","gemini-cli","cursor"] dependencies {"python":["build>=1.0","pytest>=7.4","pytest-cov>=4.1","sphinx>=7.2","numpy>=1.24","setuptools>=68"]} last_updated 2026-03-17 status stable
Python Research Package Development
When to Use This Skill
Use this skill when you need to:
Set up a modern Python package with pyproject.toml (PEP 517/518)
Structure a research software repository with src layout
Write unit and integration tests with pytest
Generate API documentation with Sphinx and autodoc
Publish a package to PyPI or a conda channel
Set up continuous integration (GitHub Actions) for research software
Create reproducible research packages with versioning
Trigger keywords : Python package, pyproject.toml, setuptools, build, wheel, pytest, coverage, Sphinx, autodoc, Read the Docs, PyPI, conda-forge, research software engineering, FAIR software, src layout, namespace package, entry points, semantic versioning.
Background & Key Concepts
Modern Python Packaging (PEP 517/518)
pyproject.toml is the single source of truth:
[build-system]: specifies build backend (setuptools, flit, poetry)[project]: package metadata (name, version, dependencies)[project.optional-dependencies]: optional extras[project.scripts]: CLI entry points
Semantic Versioning
MAJOR.MINOR.PATCH (e.g., 1.2.3):
MAJOR: breaking API changes
MINOR: backward-compatible new features
PATCH: backward-compatible bug fixes
Use __version__ = "1.0.0" in src/mypackage/__init__.py.
Src Layout
Placing code in src/mypackage/ prevents accidental imports from the project root and enforces installation before use:
mypackage/
├── src/
│ └── mypackage/
│ ├── __init__.py
│ └── core.py
├── tests/
│ └── test_core.py
├── docs/
│ └── conf.py
└── pyproject.toml
Test Coverage
Coverage measures the fraction of code lines executed during tests. Target ≥ 80% for research packages. Use pytest-cov:
pytest --cov=src/mypackage --cov-report=html
Environment Setup
pip install build>=1.0 pytest>=7.4 pytest-cov>=4.1 sphinx>=7.2 \
twine>=4.0 setuptools>=68
Core Workflow
Step 1: Package Structure and pyproject.toml
mkdir -p my_research_package/src/my_research_package
mkdir -p my_research_package/tests
mkdir -p my_research_package/docs
cd my_research_package
"""My Research Package: Tools for quantitative analysis."""
__version__ = "0.1.0"
__author__ = "Research Team"
__email__ = "research@university.edu"
from .core import (
DataProcessor,
StatisticalAnalyzer,
compute_effect_size,
)
__all__ = ["DataProcessor" , "StatisticalAnalyzer" , "compute_effect_size" ]
"""Core analysis functions for my_research_package."""
import numpy as np
import pandas as pd
from typing import Optional , Union , List
class DataProcessor :
"""Preprocess and validate research datasets.
Args:
data: Input DataFrame or array-like
missing_strategy: How to handle missing values.
One of 'drop', 'mean', 'median', 'zero'.
"""
VALID_STRATEGIES = ("drop" , "mean" , "median" , "zero" )
def __init__ (
self,
data: Union [pd.DataFrame, np.ndarray],
missing_strategy: str = "mean" ,
):
if missing_strategy not in self .VALID_STRATEGIES:
raise ValueError(
f"missing_strategy must be one of {self.VALID_STRATEGIES} , "
f"got '{missing_strategy} '"
)
self .missing_strategy = missing_strategy
self ._data = self ._validate_input(data)
def _validate_input (self, data ):
"""Validate and convert input to DataFrame."""
if isinstance (data, pd.DataFrame):
return data.copy()
elif isinstance (data, np.ndarray):
if data.ndim == 1 :
return pd.DataFrame(data, columns=["value" ])
return pd.DataFrame(data)
else :
raise TypeError(f"Expected DataFrame or ndarray, got {type (data)} " )
def process (self ) -> pd.DataFrame:
"""Apply missing value strategy and return cleaned data.
Returns:
pd.DataFrame: Cleaned dataset.
"""
df = self ._data.copy()
if self .missing_strategy == "drop" :
return df.dropna()
elif self .missing_strategy == "mean" :
return df.fillna(df.mean(numeric_only=True ))
elif self .missing_strategy == "median" :
return df.fillna(df.median(numeric_only=True ))
elif self .missing_strategy == "zero" :
return df.fillna(0 )
@property
def shape (self ):
"""Return (rows, columns) of the dataset."""
return self ._data.shape
@property
def missing_count (self ):
"""Return total number of missing values."""
return int (self ._data.isna().sum ().sum ())
class StatisticalAnalyzer :
"""Compute descriptive and inferential statistics.
Args:
data: Input array-like of values
"""
def __init__ (self, data: Union [np.ndarray, List [float ], pd.Series] ):
self .data = np.asarray(data, dtype=float )
def describe (self ) -> dict :
"""Return descriptive statistics.
Returns:
dict: n, mean, std, min, q25, median, q75, max
"""
d = self .data[~np.isnan(self .data)]
if len (d) == 0 :
return {}
return {
"n" : len (d),
"mean" : float (np.mean(d)),
"std" : float (np.std(d, ddof=1 )),
"min" : float (np.min (d)),
"q25" : float (np.percentile(d, 25 )),
"median" : float (np.median(d)),
"q75" : float (np.percentile(d, 75 )),
"max" : float (np.max (d)),
}
def confidence_interval (self, alpha: float = 0.05 ) -> tuple :
"""Compute (1-alpha)% confidence interval for the mean.
Args:
alpha: Significance level (default 0.05 for 95% CI)
Returns:
(lower, upper) confidence interval tuple
"""
from scipy import stats
d = self .data[~np.isnan(self .data)]
n = len (d)
if n < 2 :
raise ValueError("Need at least 2 observations for CI" )
se = stats.sem(d)
h = se * stats.t.ppf(1 - alpha / 2 , df=n - 1 )
mean = np.mean(d)
return (float (mean - h), float (mean + h))
def compute_effect_size (
group1: Union [np.ndarray, List [float ]],
group2: Union [np.ndarray, List [float ]],
method: str = "cohens_d" ,
) -> float :
"""Compute effect size between two groups.
Args:
group1: Observations from first group
group2: Observations from second group
method: Effect size measure. One of 'cohens_d', 'glass_delta', 'hedges_g'
Returns:
Effect size value (positive = group1 > group2)
Raises:
ValueError: If method is not recognized
"""
g1 = np.asarray(group1, dtype=float )
g2 = np.asarray(group2, dtype=float )
mean_diff = np.mean(g1) - np.mean(g2)
n1, n2 = len (g1), len (g2)
if method == "cohens_d" :
pooled_var = ((n1 - 1 ) * np.var(g1, ddof=1 ) +
(n2 - 1 ) * np.var(g2, ddof=1 )) / (n1 + n2 - 2 )
return float (mean_diff / np.sqrt(pooled_var))
elif method == "glass_delta" :
return float (mean_diff / np.std(g2, ddof=1 ))
elif method == "hedges_g" :
d = compute_effect_size(g1, g2, method="cohens_d" )
j = 1 - 3 / (4 * (n1 + n2 - 2 ) - 1 )
return float (d * j)
else :
raise ValueError(f"Unknown method '{method} '. "
f"Choose from: cohens_d, glass_delta, hedges_g" )
[build-system]
requires = ["setuptools>=68" , "wheel" ]
build-backend = "setuptools.backends.legacy:build"
[project]
name = "my-research-package"
version = "0.1.0"
description = "Tools for quantitative research analysis"
readme = "README.md"
license = {text = "MIT" }
authors = [
{name = "Research Team" , email = "research@university.edu" },
]
keywords = ["research" , "statistics" , "data analysis" ]
classifiers = [
"Development Status :: 3 - Alpha" ,
"Intended Audience :: Science/Research" ,
"License :: OSI Approved :: MIT License" ,
"Programming Language :: Python :: 3" ,
"Programming Language :: Python :: 3.9" ,
"Programming Language :: Python :: 3.10" ,
"Programming Language :: Python :: 3.11" ,
]
requires-python = ">=3.9"
dependencies = [
"numpy>=1.24" ,
"pandas>=2.0" ,
"scipy>=1.11" ,
]
[project.optional-dependencies]
viz = ["matplotlib>=3.7" ]
dev = [
"pytest>=7.4" ,
"pytest-cov>=4.1" ,
"sphinx>=7.2" ,
"sphinx-rtd-theme>=1.3" ,
"twine>=4.0" ,
]
[project.urls]
Homepage = "https://github.com/example/my-research-package"
Documentation = "https://my-research-package.readthedocs.io"
Repository = "https://github.com/example/my-research-package"
[tool.setuptools.packages.find]
where = ["src" ]
[tool.pytest.ini_options]
testpaths = ["tests" ]
addopts = "--cov=src/my_research_package --cov-report=term-missing"
[tool.coverage.run]
source = ["src/my_research_package" ]
[tool.coverage.report]
exclude_lines = [
"pragma: no cover" ,
"if __name__ == .__main__.:" ,
]
Step 2: Testing with Pytest
"""Tests for my_research_package core module."""
import pytest
import numpy as np
import pandas as pd
import sys, os
sys.path.insert(0 , os.path.join(os.path.dirname(__file__), ".." , "src" ))
from my_research_package.core import DataProcessor, StatisticalAnalyzer, compute_effect_size
class TestDataProcessor :
"""Tests for DataProcessor class."""
def setup_method (self ):
"""Set up test fixtures."""
self .clean_data = pd.DataFrame({"a" : [1.0 , 2.0 , 3.0 ], "b" : [4.0 , 5.0 , 6.0 ]})
self .missing_data = pd.DataFrame({"a" : [1.0 , np.nan, 3.0 ], "b" : [np.nan, 5.0 , 6.0 ]})
def test_basic_initialization (self ):
"""Test DataProcessor initializes with valid input."""
dp = DataProcessor(self .clean_data)
assert dp.shape == (3 , 2 )
assert dp.missing_count == 0
def test_missing_count (self ):
"""Test missing count is correctly reported."""
dp = DataProcessor(self .missing_data)
assert dp.missing_count == 2
def test_mean_imputation (self ):
"""Test mean imputation strategy."""
dp = DataProcessor(self .missing_data, missing_strategy="mean" )
result = dp.process()
assert result.isna().sum ().sum () == 0
assert result.loc[1 , "a" ] == pytest.approx(2.0 )
def test_drop_strategy (self ):
"""Test drop missing strategy removes rows with NaN."""
dp = DataProcessor(self .missing_data, missing_strategy="drop" )
result = dp.process()
assert len (result) == 1
def test_invalid_strategy_raises (self ):
"""Test ValueError on invalid strategy."""
with pytest.raises(ValueError, match ="missing_strategy must be one of" ):
DataProcessor(self .clean_data, missing_strategy="invalid" )
def test_numpy_array_input (self ):
"""Test DataProcessor accepts numpy arrays."""
arr = np.array([1 , 2 , 3 ])
dp = DataProcessor(arr)
assert dp.shape == (3 , 1 )
def test_invalid_input_type_raises (self ):
"""Test TypeError on invalid input type."""
with pytest.raises(TypeError):
DataProcessor([1 , 2 , 3 ])
class TestStatisticalAnalyzer :
"""Tests for StatisticalAnalyzer class."""
def setup_method (self ):
"""Set up test fixtures."""
np.random.seed(42 )
self .data = np.random.normal(10 , 2 , 100 )
def test_describe_output_keys (self ):
"""Test describe() returns expected keys."""
sa = StatisticalAnalyzer(self .data)
result = sa.describe()
expected_keys = {"n" , "mean" , "std" , "min" , "q25" , "median" , "q75" , "max" }
assert set (result.keys()) == expected_keys
def test_describe_mean_approx (self ):
"""Test mean is approximately correct."""
sa = StatisticalAnalyzer(self .data)
result = sa.describe()
assert result["mean" ] == pytest.approx(np.mean(self .data))
def test_confidence_interval_coverage (self ):
"""Test CI width makes statistical sense."""
sa = StatisticalAnalyzer(self .data)
lo, hi = sa.confidence_interval(alpha=0.05 )
assert lo < hi
assert lo < np.mean(self .data) < hi
def test_ci_requires_minimum_data (self ):
"""Test CI raises ValueError for insufficient data."""
sa = StatisticalAnalyzer([5.0 ])
with pytest.raises(ValueError, match ="at least 2" ):
sa.confidence_interval()
def test_nan_ignored_in_describe (self ):
"""Test NaN values are excluded from computations."""
data_with_nan = np.array([1.0 , 2.0 , np.nan, 4.0 , 5.0 ])
sa = StatisticalAnalyzer(data_with_nan)
result = sa.describe()
assert result["n" ] == 4
class TestComputeEffectSize :
"""Tests for compute_effect_size function."""
def setup_method (self ):
"""Set up test groups with known effect size."""
np.random.seed(42 )
self .g1 = np.random.normal(10 , 2 , 50 )
self .g2 = np.random.normal(8 , 2 , 50 )
def test_cohens_d_positive (self ):
"""Test Cohen's d is positive when group1 > group2."""
d = compute_effect_size(self .g1, self .g2, method="cohens_d" )
assert d > 0
def test_cohens_d_symmetric (self ):
"""Test that reversing groups negates the effect size."""
d1 = compute_effect_size(self .g1, self .g2, method="cohens_d" )
d2 = compute_effect_size(self .g2, self .g1, method="cohens_d" )
assert d1 == pytest.approx(-d2, abs =1e-10 )
def test_hedges_g_smaller_than_d (self ):
"""Test Hedges' g is smaller than Cohen's d in magnitude."""
d = abs (compute_effect_size(self .g1, self .g2, method="cohens_d" ))
g = abs (compute_effect_size(self .g1, self .g2, method="hedges_g" ))
assert g < d
def test_unknown_method_raises (self ):
"""Test ValueError on unknown method."""
with pytest.raises(ValueError, match ="Unknown method" ):
compute_effect_size(self .g1, self .g2, method="unknown_es" )
@pytest.mark.parametrize("method" , ["cohens_d" , "glass_delta" , "hedges_g" ]
def test_all_methods_return_float (self, method ):
"""Test all methods return a float."""
result = compute_effect_size(self .g1, self .g2, method=method)
assert isinstance (result, float )
if __name__ == "__main__" :
pytest.main([__file__, "-v" , "--tb=short" ])
Step 3: Documentation Setup with Sphinx
cd docs
sphinx-quickstart --quiet --project "My Research Package" \
--author "Research Team" --release "0.1.0" \
--language en --ext-autodoc --ext-napoleon \
--ext-viewcode --makefile --no-batchfile
import os
import sys
sys.path.insert(0 , os.path.abspath("../src" ))
project = "My Research Package"
copyright = "2026, Research Team"
author = "Research Team"
release = "0.1.0"
extensions = [
"sphinx.ext.autodoc" ,
"sphinx.ext.napoleon" ,
"sphinx.ext.viewcode" ,
"sphinx.ext.intersphinx" ,
"sphinx.ext.mathjax" ,
]
napoleon_google_docstring = True
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_include_private_with_doc = False
autodoc_default_options = {
"members" : True ,
"undoc-members" : False ,
"show-inheritance" : True ,
"special-members" : "__init__" ,
}
intersphinx_mapping = {
"python" : ("https://docs.python.org/3" , None ),
"numpy" : ("https://numpy.org/doc/stable" , None ),
"pandas" : ("https://pandas.pydata.org/docs" , None ),
}
html_theme = "sphinx_rtd_theme"
.. File: docs/api.rst
API Reference
=============
Core Module
-----------
.. automodule:: my_research_package.core
:members:
:undoc-members:
:show-inheritance:
DataProcessor
~~~~~~~~~~~~~
.. autoclass:: my_research_package.core.DataProcessor
:members:
:special-members: __init__
StatisticalAnalyzer
~~~~~~~~~~~~~~~~~~~
.. autoclass:: my_research_package.core.StatisticalAnalyzer
:members:
:special-members: __init__
Functions
~~~~~~~~~
.. autofunction:: my_research_package.core.compute_effect_size
Advanced Usage
GitHub Actions CI/CD Pipeline
name: CI
on:
push:
branches: [main , develop ]
pull_request:
branches: [main ]
jobs:
test:
name: Test Python ${{ matrix.python-version }}
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.9" , "3.10" , "3.11" ]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install package in development mode
run: |
python -m pip install --upgrade pip
pip install -e ".[dev]"
- name: Run tests with coverage
run: |
pytest --cov=src/my_research_package \
--cov-report=xml --cov-report=term-missing \
-v
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v3
with:
file: ./coverage.xml
fail_ci_if_error: false
publish:
name: Publish to PyPI
needs: test
runs-on: ubuntu-latest
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v' )
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4
with:
python-version: "3.11"
- name: Build distribution
run: |
pip install build
python -m build
- name: Publish to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
password: ${{ secrets.PYPI_API_TOKEN }}
Programmatic Version Bumping
"""Script to bump version in pyproject.toml and __init__.py."""
import re
import sys
import os
def bump_version (version_type="patch" ):
"""Bump semantic version.
Args:
version_type: 'major', 'minor', or 'patch'
"""
init_path = os.path.join("src" , "my_research_package" , "__init__.py" )
with open (init_path) as f:
content = f.read()
match = re.search(r'__version__ = "(\d+)\.(\d+)\.(\d+)"' , content)
if not match :
raise ValueError("Could not find version string" )
major, minor, patch = int (match .group(1 )), int (match .group(2 )), int (match .group(3 ))
if version_type == "major" :
major += 1 ; minor = 0 ; patch = 0
elif version_type == "minor" :
minor += 1 ; patch = 0
elif version_type == "patch" :
patch += 1
else :
raise ValueError(f"Unknown version_type: {version_type} " )
new_version = f"{major} .{minor} .{patch} "
new_content = content.replace(match .group(0 ), f'__version__ = "{new_version} "' )
with open (init_path, "w" ) as f:
f.write(new_content)
pyproject_path = "pyproject.toml"
with open (pyproject_path) as f:
proj_content = f.read()
old_ver_str = f'version = "{major-1 if version_type=="major" else major} .'
old_v = match .group(0 ).replace("__version__ = " , "version = " )
proj_content = proj_content.replace(
f'version = "{match .group(1 )} .{match .group(2 )} .{match .group(3 )} "' ,
f'version = "{new_version} "'
)
with open (pyproject_path, "w" ) as f:
f.write(proj_content)
print (f"Version bumped to {new_version} " )
return new_version
if __name__ == "__main__" :
vtype = sys.argv[1 ] if len (sys.argv) > 1 else "patch"
bump_version(vtype)
Troubleshooting Problem Cause Fix ModuleNotFoundError in testssrc not in PYTHONPATH Install in editable mode: pip install -e . Sphinx autodoc finds no members Wrong sys.path in conf.py Verify sys.path.insert(0, "../src") pytest import error Conflicting package installations Use python -m pytest instead of plain pytest Build fails: missing wheel build backend misconfigured Install build: pip install build; run python -m build PyPI upload fails Token not set Create API token at pypi.org; store as environment variable Coverage < 80% Untested branches Add tests for edge cases; use --cov-branch flag
External Resources
Examples
Example 1: CLI Entry Point for a Research Tool
"""Command-line interface for my_research_package."""
import argparse
import sys
import numpy as np
from .core import StatisticalAnalyzer, compute_effect_size
def main ():
"""Entry point for the research analysis CLI."""
parser = argparse.ArgumentParser(
description="Compute statistics for research data" ,
formatter_class=argparse.RawDescriptionHelpFormatter,
)
subparsers = parser.add_subparsers(dest="command" )
desc_parser = subparsers.add_parser("describe" , help ="Compute descriptive statistics" )
desc_parser.add_argument("--values" , nargs="+" , type =float , required=True ,
help ="Space-separated values" )
es_parser = subparsers.add_parser("effect-size" , help ="Compute effect size" )
es_parser.add_argument("--group1" , nargs="+" , type =float , required=True )
es_parser.add_argument("--group2" , nargs="+" , type =float , required=True )
es_parser.add_argument("--method" , default="cohens_d" ,
choices=["cohens_d" , "glass_delta" , "hedges_g" ])
args = parser.parse_args()
if args.command == "describe" :
sa = StatisticalAnalyzer(args.values)
stats = sa.describe()
for k, v in stats.items():
print (f"{k} : {v:.4 f} " if isinstance (v, float ) else f"{k} : {v} " )
elif args.command == "effect-size" :
es = compute_effect_size(args.group1, args.group2, method=args.method)
print (f"{args.method} = {es:.4 f} " )
else :
parser.print_help()
sys.exit(1 )
if __name__ == "__main__" :
main()
[project.scripts]
research-analyze = "my_research_package.cli:main"
Example 2: Automated Package Testing
pytest tests/ -v --cov=src/my_research_package \
--cov-report=html --cov-report=term-missing \
--tb=short 2>&1 | head -50
python -m build
ls dist/
twine check dist/*
pip install dist/*.whl
python -c "import my_research_package; print(my_research_package.__version__)"
